Investigation of an outbreak of Shiga-toxigenic Escherichia coli

This week's issue of the Journal of the American Medical Association reports on a culture-independent sequence-based metagenomics approach in the investigation of an outbreak of Shiga-toxigenic Escherichia coli.

Identification of the bacterium responsible for an outbreak can aid in disease management.

However, traditional culture-based diagnosis can be difficult, particularly if no specific diagnostic test is available for an outbreak strain.

Dr Nicholas Loman and colleagues explored the potential of metagenomics, which is the direct sequencing of DNA extracted from microbiologically complex samples, as an open-ended clinical discovery platform capable of identifying and characterizing bacterial strains from an outbreak without laboratory culture.

In a retrospective investigation, 45 samples were selected from fecal specimens obtained from patients with diarrhea during the 2011 outbreak of Shiga-toxigenic Escherichia coli O104:H4 in Germany.

The researchers noted that samples were subjected to high-throughput sequencing, followed by a 3-phase analysis.

In phase 1, a de novo assembly approach was developed to obtain a draft genome of the outbreak strain.

The team of doctors assessed that in phase 2, the depth of coverage of the outbreak strain genome was determined in each sample.

In phase 3, sequences from each sample were compared with sequences from known bacteria to identify pathogens other than the outbreak strain.

The outbreak strain genome was recovered from 10 samples at greater than 10-fold coverage

JAMA

The team's main outcomes included the recovery of genome sequence data for the purposes of identification and characterization of the outbreak strain and other pathogens from fecal samples.

During phase 1, a draft genome of the Shiga-toxigenic Escherichia coli outbreak strain was obtained.

The doctors reported that during phase 2, the outbreak strain genome was recovered from 10 samples at greater than 10-fold coverage, and from 26 samples at greater than 1-fold coverage.

Sequences from the Shiga-toxin genes were detected in 27 of 40 Shiga-toxigenic Escherichia coli-positive samples.

The research team noted that in phase 3, sequences from Clostridium difficile, Campylobacter jejuni, Campylobacter concisus, and Salmonella enterica were recovered.

Dr Loman's team commented "These results suggest the potential of metagenomics as a culture-independent approach for the identification of bacterial pathogens during an outbreak of diarrheal disease."

"Challenges include improving diagnostic sensitivity, speeding up and simplifying workflows, and reducing costs."